Consumers with the least amount of money are often the ones shelling out the most, the study found. The average "cash-strapped consumer," or people whose accounts frequently dip into negative territory and who lack lines of credit or a savings account to provide a buffer, can end up incurring about $470 in annual fees.

Bank fees mean big bucks for financial institutions

One rule of thumb when searching for checking accounts that save money is to look at credit unions and online-only banks.

"We've actually seen the cost of checking accounts increase over the past couple of years," noted Jill Gonzalez, a spokeswoman for WalletHub. "Usually online-only banks typically have the lowest fees because they don't have the same type of overhead. They have a younger consumer in mind."

Those banks include Ally Bank, which ranked No. 2 in affordability, just after Capital One. While Ally's checking account might not be suitable for wealthier consumers looking for service, it may appeal to younger consumers who are living from paycheck to paycheck because its Ally Bank Interest Checking Account has no monthly fee. One downside to online-only accounts, Gonzalez noted, is that some don't provide paper checks.

On the other end of the spectrum are premium checking accounts, which often throw in perks such as no-fee out-of-network ATM withdrawals, according to SmartAsset. The downside is that many require large balances -- from $25,000 to $50,000 -- to open a premium account.

Bank fees rising higher than ever before, study says

One of the study's most surprising findings is the potential to make money from your checking account, Gonzalez said. One account, the Santander extra20 Checking account, pays $20 to consumers who have a direct deposit of more than $1,500 as well as two online bill payments each month.

"Most consumers wouldn't even know they could get rewarded," she said. "The banking landscape is so competitive, and banks really want people to open accounts with them before more uncertainties arise later this year," when the Federal Reserve is expected to boost interest rates.

So, how can you dig up the details of each checking account? It's not all that simple, WalletHub found in a separate study about checking account transparency. The average checking account has about 25 fees, with most banks ranging between 20 to 40. But some had almost 50.

There's also no uniform disclosure format for fees, which can make it confusing for consumers to figure out a checking account's costs and comparison shop. These findings echo a study published earlier this year from The Pew Charitable Trusts, which found many banks don't make it easy for consumers to find out their policies on fees and dispute resolution.

One red flag is language that promises a full fee disclosure only after the consumer has signed on for an account, WalletHub said. Gonzalez estimated that about half of banks use that technique.

The bottom line is that banking customers need to be on their toes when shopping for a new checking account. Said Gonzalez: "Not all fees are disclosed."